Sigma-Aldrich does about 60 percent of its revenue overseas and 40 percent in the U.S., thus subjecting the company to foreign taxes on sales outside the U.S. and then 35 percent in federal taxes on money brought back to the U.S.

Asked if the structure of the deal would eliminate that double taxation, Merck Executive Board Chairman Karl-Ludwig Kley said in a CNBC "Squawk Box" interview: "We pay taxes in every country to where we are. We are not a company looking for tax havens."

He said the company's effective tax rate is about 25 percent or 26 percent. Germany's effective corporate rate, including local taxes, is 29.58 percent, according to KPMG.

"Tax is the last consideration," he added shortly after the announcement. "We look at the commercial fit. We look at the business opportunities. Then you have to take into account issues like labor costs ... [and] infrastructure costs. For example you have low energy costs compared to Europe."

Sigma-Aldrich CEO Rakesh Sachdev said: "We pay an effective tax rate of about 28 percent, 29 percent, which is on the high side of most life sciences companies." But this a business deal, not a tax advantage transaction, he said.

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